A witness at a child sex abuse inquiry says she was raped "well over 100 times" by a priest at St Joseph's Neerkol Orphanage Rockhampton in central Queensland.

The Royal Commission into Institutional Responses to Child Sexual Abuse has heard the treatment of children at the orphanage was "vicious and sadistic", while an earlier inquiry found hundreds of children were sexually abused, beaten and forced into hard labour there.

The inquiry has begun hearings into how the Sisters of Mercy, the Rockhampton diocese and the state government responded to complaints made by former residents of St Joseph's Neerkol Orphanage.

The orphanage has already been the subject of several police and government investigations, and a 1999 inquiry led by former Queensland governor Leneen Forde.

After the so-called Forde Inquiry, the Queensland government at the time offered ex gratia payments of up to $40,000 to people as long as they dropped other legal action against the state.

Over the next two weeks, the royal commission will hear evidence from 18 witnesses, with 13 being former residentsof the orphanage, who say they were abused by priests, workers, and nuns there from 1940 to 1975.

Abuse started on Christmas Eve

A witness, known as AYB, told the inquiry how she was abused by a former priest at the orphanage, Father Reginald Basil Durham.

She said the abuse started when she was 11 years old and Father Durham came to the family home on Christmas Eve to drop off some presents.

I felt so powerless, so robotic. He had so much power over me. I believed that I did not have choices. It was almost like being enslaved.

Witness AYB

AYB said she was under the house with Father Durham when he said he deserved a kiss from bringing her presents.

"Father Durham then kissed me using his tongue and fondled my breasts and told me that I was his special little girl," she said.

"He was a smoker and the taste was horrible.

"He told me it was to be 'our secret' and I was not to tell anyone.

All I could focus on was the crosses on his shirt, so I yelled at him, 'Father, you are committing a mortal sin'.

Witness Mary Adams

"I could hear his heart beating.

"Father Durham had sexually abused and raped me well over 100 times.

"I felt so powerless, so robotic. He had so much power over me.

"I believed that I did not have choices. It was almost like being enslaved."

She said Father Durham would sometimes take her down to an old toilet block.

AYB said she was forced to rub his body and Father Durhan raped her — which he said was to prepare her for when she had a baby.

"Even today there are times when I experience nightmares and call out in my sleep 'go away, stop and don't touch me'," she said.

"I am doing this so we can claim our lives back to try and live out the rest of our lives with courage and peace and without the demons from the past dominating our memories with shame, guilt and regret."

Second witness raped, badly beaten

Former resident Mary Adams was sent to Neerkol when she was just nine months old.

She told the inquiry that she was sexually abused by two priests.

"I had become hysterical, crying, trying to push him off me," she said.

"All I could focus on was the crosses on his shirt, so I yelled at him, 'Father, you are committing a mortal sin'."

Ms Adams, 64, also broke down as she addressed the hard punishments dished out by nuns.

Sobbing at times, Ms Adams told the hearing she was punched, slapped, and pulled by her hair by one sister.

She said on another occasion she was flogged with a skipping rope so hard she struggled to walk for days.

"I had welts on my body for days after," she said.

Children too scared to tell their stories of abuse

Counsel assisting the royal commission Sophie David SC told the hearing in her opening address that one former resident of the orphanage had described the treatment by the sisters as "vicious and sadistic".

She said at the time, the childrenwere too scared to tell their stories because they were afraid of harsh punishment.

She said as a result there were criminal proceedings in respect of Father Durham, now deceased, and a former employee of the orphanage, Kevin Baker.

The court heard Queensland Police charged Father Durham on February 6, 1997 with 40 sexual offences against five former residents of the orphanage and a former member of his parish.

On February 15, 1999, Father Durham pleaded guilty to six counts of indecently dealing with a former resident, identified by the inquiry as AYB.

All other charges were discontinued and he was sentenced to 18 months in prison, with a recommendation for release on parole after a period of four months.

The hearing was told that on March 31, 1998, Mr Baker, who was an employee of the orphanage as well as being a former resident, was committed for trial on 69 mainly sexual offences, related to 12 former residents.